rs6815517

Variant names:

• chr4-109808933-C-T
• rs6815517

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.719 in 152,016 control chromosomes in the GnomAD database, including 39,523 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (39523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109232 AN: 151898 Hom.: 39480 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.693

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.719 AC: 109328 AN: 152016 Hom.: 39523 Cov.: 31 AF XY: 0.720 AC XY: 53532 AN XY: 74304

African (AFR) AF: 0.733 AC: 30374 AN: 41450

American (AMR) AF: 0.623 AC: 9514 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2427 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4607 AN: 5186

South Asian (SAS) AF: 0.806 AC: 3884 AN: 4820

European-Finnish (FIN) AF: 0.713 AC: 7508 AN: 10532

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48775 AN: 67980

Other (OTH) AF: 0.696 AC: 1466 AN: 2106

Alfa AF: 0.703 Hom.: 6490

Bravo AF: 0.709

Asia WGS AF: 0.813 AC: 2826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.33
PhyloP100		-0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6815517; hg19: chr4-110730089;